Gone So Long
by Dr. Anthro-Tano
Summary: After the TNoTD, The Doctor disappears for five years after his and Clara's relationship becomes a little deeper than friends. He drops her off in the wrong place, and it turns Clara's world upside down. When he comes back Clara has moved on with her life, and a tragedy a year before the Doctor came back casts a dark shadow over Clara and others. Bad summary good story.
1. Prologue

**AUTHOR'S NOTE: ****Okay, so this story might seem complicated at first. Well, it will seem complicated when you start chapter one. This is kinda like a back story to explain everything first. Kinda…I think. Well, anyways this is the prologue for **_**Gone So Long**_** and will be chapter one for **_**Wasting All These Tears**_**. Yes, these are the names of songs. The songs fit so that's what I'm naming them after. I'll explain everything in the author's note for chapter one. So! Let the story begin!**

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For a week or two, the Doctor kept Clara on the TARDIS, but even though she could ask to leave whenever she wanted, she knew she should stay. They both needed the comfort only the other could provide, and they frequently found themselves clinging to each other with Clara's face buried into the Doctor's chest while the Doctor's nose was pressed into the top of her head, into her hair.

Their relationship changed one night, or what passed for night time, when Clara awoke screaming and crying from a nightmare, and the Doctor rushed to her side. The Doctor had held her and rocked her, but as he leaned down to kiss her forehead, she lifted her face up to look at him, and their lips met.

The kiss lasted longer than it should have, and although his hands twitched a little, the Doctor didn't flail like he usually did whenever he was kissed without warning. When they finally separated, they just stared at each other in shock for a few moments until the Doctor swallowed nervously and stammered, "I-I-I…I didn't…"

"Shut up…" Clara murmured as she wrapped her arms around his neck and pulled him back to her, pressing her lips against his again. The Doctor's hands began to twitch again, resisting the urge to flap his arms, but he soon began to calm down as his hands landed on her waist and held her closer. Clara leaned back, laying back down as she pulled him along with her and continued to kiss him. That night they let go of their doubts and fears and showed each other what they felt and how much they loved each other.

Clara awoke the next morning, and the Doctor wasn't lying next to her like she expected him to be. After putting on some clothes, she went looking for the Doctor, finding him in the central console room as he leaned against it and stared off into space, obviously deep in thought.

"Doctor?" Clara called softly as she approached him, her brow furrowing together in worry. The Doctor didn't seem to hear her as he began to mess with a few knobs and dials and flipped a few switches.

"Doctor," Clara called again, this time a little louder as she stepped closer to him and placed a hand on his arm.

"I'm taking you home," the Doctor stated softly, refusing to look at her as he went around the center console and continued to mess with the controls. Clara froze as she watched him and began to ask, "Wha…"

"Clara, please…Don't make this any harder than it needs to be…"

Clara was confused and hurt as tears welled up in her eyes. What had she done wrong? Did he regret what they did? Was that all he had wanted: one and done? Were his whispers of love the night before just spur of the moment ramblings?

The Doctor saw the look on her face and the tears threatening to spill in her eyes, and his heart broke at the pain and hurt he saw there. He moved towards her and reached out to touch her cheek as he commented, "No, I don't…"

"Just let me know when we get there…" Clara interrupted, her heart break cracking her voice as she pushed his hand away and turned around, leaving him there in that room alone.

The Doctor cursed himself and slammed his fist down onto the console. He couldn't possibly imagine what thoughts were going through her mind or what she thought of him. He took a deep breath and reached out, pulling the throttle lever as even the TARDIS hesitated to take off. The TARDIS could hear what the Doctor couldn't and knew that Clara was crying. She could sense the pain and betrayal the girl felt.

Once the ship landed, the Doctor waited a few moments with his eyes closed as he regained his composure and went to find Clara. He knocked on her door and called softly, "Clara…We're here…"

The door opened moments later as Clara emerged and whisked past him. The Doctor reached out to grab her arm as he exclaimed, "Clara, wait! Please!"

Clara stopped, but didn't turn around as the Doctor approached her from behind and placed his hands on her shoulders. He heard a sob escape her as her shoulders shook, and she lowered her head. The Doctor turned her around holding her gently by her upper arms as he looked down at her, but her head was still down, and her hair fell forward, hiding her eyes.

"Clara…" The Doctor took her chin and lifted her face so he could look into her eyes. The pain he saw there broke both of his hearts as he moved his hand and stroked her cheek with his thumb, brushing away her tears. Clara couldn't help but lean into his touch as she closed her eyes and let him pull her closer.

The Doctor kissed her forehead and rested his chin on top of her head as he assured quietly, "This isn't goodbye…I promise…I just want you to think this over before you commit. You need to think over things. Okay?"

Clara opened her eyes to look up at him as she nodded and replied, "Okay…"

The Doctor took her hand and led her to the console room as tears built up in Clara's eyes again. She didn't want to leave. She didn't need to think over things. This was what she wanted. _This_ was the only thing she _needed_. However, when she looked up at him, she could see the pain and second thoughts in his eyes and knew he thought he was doing the right thing.

When they reached the center console the, Doctor turned Clara around so she was facing him as he leaned down and pressed his lips against hers. Clara's eyes fluttered shut as she stood up on the tips of her toes and leaned into the kiss. When they finally separated, Clara wrapped her arms around his middle and buried her face into his chest as she whispered, "Don't make me go…"

"Clara, come on…" The Doctor responded as he stroked her hair, not wanting to let her go himself. "It'll only be a week…"

"You promise?"

"I promise," the Doctor replied softly as he let go of her in order to cross both of his hearts with his fingers. Clara nodded as she took a deep breath and turned around. The Doctor didn't walk her to the entrance, but instead stayed back and watched after her, having a bad feeling that this was goodbye. He forced a smile when she looked over her shoulder at him and asked with uncertainty in her voice, "See you in a week?"

The Doctor gave her a reassuring smile and dipped his head in affirmation as he replied, "See you in a week."

With that, Clara turned and pushed open the doors, taking a step out as she closed the doors behind her. Her first thought was registering that it was raining, _pouring_ actually. She had forgotten how cold it had been before she went with the Doctor. However, as she wiped the water from her eyes and held her arm above them to shield them from the rain so she could see, she realized that her surroundings were unfamiliar to her. This was _not_ the Maitland house.

"Doctor, we're not—" Clara began to call as she started to turn around, reaching up to grab the key to the TARDIS that was hanging on a necklace around her neck. However, to her great dismay, the TARDIS engines had already started to whine and turn as the time machine pulsed out of existence right as Clara's hand pressed against it. Her hand fell through into the empty space that had just been occupied by the TARDIS.

"Great…" Clara mumbled as she crossed her arms across her chest in an effort to keep warm, looking around to try to see if she could figure out where she was. There were no familiar land marks, any known markers, or anything remotely familiar except for the fact that she was pretty sure she could hear the sound of the ocean and waves hitting the shore through the downpour.

There was one house, well _mansion_, that Clara could see, and she'd rather take her chances with whoever lived there and get out of the rain than staying out in the pouring rain. She let out an exasperated breath and approached the large house as quick as she could without slipping on the loose, wet gravel. She eagerly climbed up the stairs onto the front porch, thankful for the shelter from the rain.

After a few hesitant and unsure moments, Clara reached up and rung the doorbell before quickly withdrawing her hand as she tucked it under her other arm for warmth. She felt and heard footsteps approaching the door as a young woman's face appeared in the window beside the door to see who it was, before disappearing again. There was the sound of the lock being unlatched as the handle turned, and the door opened.

A young woman, a few years younger than Clara but still in her twenties, if she had to guess, with ginger hair stood there as she looked at Clara in confusion and asked, "Can I help you?"

"Y-Y-Yes, please," Clara stammered as her teeth clattered, and she shivered. "My boyfriend dropped me off, and I don't have anywhere to go or any belongings."

"Oh, you poor thing!" The girl exclaimed as she grabbed Clara and pulled her inside. She closed the door and turned as she called, "Dad! Beckett!"

The girl rubbed Clara's shoulder in an effort to warm her up as an older man in his early forties and a woman in her early to mid thirties came into the room. The man looked at Clara curiously before looking at his daughter as he asked, "Who is this, Alexis?"

"I-I-I'm…C-Clara," Clara responded for Alexis as she continued to shiver, and Alexis looked at her in sympathy. The red head grabbed a blanket that was hanging over the back of a chair near the front door and placed it around Clara's shoulder as she replied to her father's question, "She was out in the cold and has nowhere to go."

"I-I-I'm sorry f-for barging in," Clara apologized as she clutched at the blanket and pulled it tightly around herself. Kate Beckett's eyes softened as she walked forward and replied, "No, you're not barging in. Do you need a place to stay?"

"I-If you d-don't m-m-mind," Clara responded as she shivered and smiled at them gratefully, the clattering of her teeth more distinguished. She was surprised by their generosity, kindness, and friendliness; but she was intrigued by the fact that they all had American accents. Yeah, there were plenty of Americans in Britain, but it still startled her.

"We don't mind," Beckett assured with a warm smile, before she looked at the man next to her. "Do we, Castle?"

"Not at all," Richard Castle replied as he also gave a smile. "If you need a place to stay, you are welcome to stay until the end of the trip."

Clara relaxed as she sighed in relief and smiled brightly. Beckett wrapped an arm around Clara, pulling her closer as she led her to the living room and commented, "We have an extra guest room you could stay in."

"Thank you so much," Clara responded as Beckett smiled and nodded. Alexis and Castle followed after them as Castle quickly caught up with them and questioned, "So what's your story?"

"_Castle_," Beckett scolded softly as she shot a look at Castle, who blinked in surprise and asked innocently, "What?"

"Let her warm up and settle in."

"Oh…sorry," Castle flashed Clara an apologetic smile, but she gave him a reassuring grin and looked at Beckett and responded, "No, he's fine." She then turned back to Castle. "You wouldn't believe me if I told you."

Beckett smirked and mumbled something under her breath that sounded like, "Don't tell him that…"

Castle's interest instantly heightened as he followed after the two women while Alexis went to light the fire place and get Clara another blanket and something warm to drink. Pi, Alexis's boyfriend, came out of the bathroom as Castle finally convinced Clara to tell them her story about what happened and how she got there. They all gathered around, sitting on the couches and chairs as Castle's mother Martha Rogers and Beckett's father Jim Beckett joined them to listen to her story.

Normally, none of the with the exception of Castle, would have believed a story like that, but the emotion she showed while sharing what happened convinced them and showed them that she was telling the truth. Nothing shocked them more than the fact that they _knew_ what she was telling was true, but it still sounded insane and absurd.

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**AUTHOR'S NOTE:**** So! Did you like it? I hope you did! :D It's about to get real confusing though in the next chapter. I'll explain in the author's note at the beginning of the next chapter. Anyways, I hope you know what I'm talking about with Castle and Beckett. If not, go look up on Google images Castle and Beckett, and you'll see who I'm talking about. **** Also, sorry it's taking me so long to update chapter 10 for **_**Beyond Destruction**_**. It's taking me a little while to write it, but I'm almost done. So! You know the drill! If not, here it is: give me a review, and I will give you a preview into the next chapter, or, if you're lucky, I'll give you a preview for further down the line.**


	2. Chapter 1

**AUTHOR'S NOTE:**** So! We're skipping ahead five years. I'll make another story about the five years that the Doctor left Clara. It will be called **_**Wasting All These Tears**_** like I said in the author's note in the prologue. I hope this chapter is not too confusing. I'll try to explain everything the best I can. Enjoy! :D**

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Clara sighed as she took her glock handgun out of a drawer in the bureau by the door to examine it like she always did when she got home. She made sure it wasn't loaded as she turned it in her hands and took it apart piece by piece. She checked to make sure it was clean; it was so she put it back together and placed it back into the drawer before going over to the couch as she collapsed onto it.

Clara lay on her back with her legs from the knees down hung over the armrest of the couch as she stared up at the ceiling and thought over her life. It had been nearly four years since the Doctor had dropped her off in Hamptons, New York, right outside the mansion of Richard Castle, a mystery novelist. She couldn't believe how far she'd come and how much her life had changed.

Detective Kate Beckett, the woman who had welcomed Clara so warmly after Alexis had let her in, was now Kate Beckett Castle after marrying her fiancé and partner Richard Castle. After spending the week with the family on their vacation, Clara had become close with Alexis Castle and Beckett, and they even offered her to stay at Castle's place back in the city until she could get back onto her feet.

Clara had to call the Maitlands and tell them that she couldn't work for them anymore. Not only did she not have the money to pay for a flight back, but also everything back home reminded her of the Doctor. How could she possibly go back?

Beckett had noticed Clara's intelligence and quick wit and problem solving skills and knew the young Brit would make a great cop and detective. She took Clara to the shooting range under the excuse that since she now lived in New York City, it would be best to know how to defend herself and others.

About a month or two later, Beckett finally came clean about her reasoning and took Clara to the police academy, joking with Castle about how Clara could be his new muse just a little less M rated scenes. After much thinking, Clara agreed to go into the police academy, and even though it was a lot of lot of work, Clara liked it and knew she would enjoy being a cop.

Six months later, and Clara graduated from the police academy nearly the highest in her class, and Beckett, Castle, Alexis, and Pi took her to the Hamptons for the weekend to celebrate it.

Clara had held onto the empty, innocent hope that the Doctor would come back for her, but as each day passed her heart broke increasingly and her hope disintegrated more and more until finally on the last night in the Hamptons, she cried alone in her room. She felt like a weak, vulnerable child, and she hated herself for it, but she needed this, she needed the release of her emotions. Beckett came in a little while later and comforted her.

Clara got a training officer in his mid to late forties named Officer Tyler Raymond who reminded Clara of her father, and Beckett introduced her to aspiring police officer Ann Hastings who Clara was friends with now. After a few more months, Clara met another cop named Simon Luther who reminded her of the Doctor. He looked almost exactly like the Doctor with brown hair that swept across his forehead, and he stood about a foot or more taller than her.

Soon Clara and Simon grew closer and closer until one night at Castle's bar the "Old Haunt," Simon kissed Clara, and she didn't fight. Instead, she kissed him back, and let him hold her close. They started dating that night, and Beckett had smiled and said she was proud of her for moving on, but Clara looked her straight in the eyes and told her she would never truly move on.

Clara and Simon dated off and on for about a year because Clara couldn't give up her hope that the Doctor would come back for her, even though she tried hard to get over it. Even though she had not told Simon about the Doctor, he knew there was something or some_one_ was holding her back from giving her all into the relationship. He tried to win her over with actions and shows of affection which flattered Clara but it didn't, it _couldn't_ steal her heart because that would forever belong to the Doctor. Or so she thought…

A few months after they started dating, not only was Clara's world flipped upside again, but so was Simon's when they discovered what they had done. (I'm too cruel to tell y'all what it is yet. I wanna see who can figure it out first cuz I will drop hints here and there.) But what they had done wasn't bad; on the contrary, it was good. But a year after this thing that they did, it was taken away in a tragedy that threw Clara into a dark pit for a while.

Tears started to well up in Clara's eyes; she missed the Doctor so much, though she would never admit it to anyone. She missed his goofy smile and fidgety antics; she even missed his oversized chin.

There was a knock on her front door, and Clara sat up quickly as she wiped away her tears. She got up and went over to the door, unlocking it as she opened it. She froze the moment she saw who was standing there with her mouth hanging slightly open and her eyes wide open. Her throat was dry as she swallowed.

"Clara! Hello!" The man greeted warmly with a broad smile as he moved forward to hug her, but Clara took a step back away from him. His smile started to disappear when she moved away from him, and when he saw the pain in her eyes as she asked, her voice cracking, "What are you doing here, Doctor?"

"I came back for you," the Doctor replied, placing his hands on her shoulders as he pulled her closer, and he kissed her forehead. "Just like I promised." He smiled down at her.

Clara pulled away as she shrugged off his hands and responded, "_No_. You promised to return after a week."

"I know. I'm sorry. It took me a good bit of time to find you because, as you know, you're all over time and space, but I finally remembered the recent history log, and long story short, I investigated, like Strax likes to say, to find you."

"You really should delete your history…" Clara murmured, and this made the Doctor smile and cringe at the same time. It was one of his favorite phrases, but he also took as she didn't want to be found. That's when it hit him.

"How long has it been?" The Doctor whispered, but he spoke too quietly for her to hear him as she looked up at him and questioned, "What?"

The Doctor looked straight into her eyes, surprising Clara with his seriousness as he repeated softly, but loud enough for her to hear him, "For you…how long has it been?"

"Five years," Clara replied quietly, and the Doctor's face twisted in grief and sorrow as he moved forward. He enveloped her in his arms with his hand tangling in her hair as he held her as close as he could and placed his chin on top of her head. He rocked her back and forth slowly, and Clara could feel his shoulders shaking as he murmured softly in a sob to her, "Oh, Clara…my Clara…I'm so sorry…"

Clara pulled away, if only a little, so she could look up at him to see tears brimming in his eyes, and she knew he was truly upset over it. She could also see the fear in his eyes; he was afraid that she wouldn't forgive him. The mixture of adoration and pain on his face made reality crash into her as relief and affection flooded her system, but she fought it, at least, at first she did. He left her, _abandoned_ her for _five_ years. She shouldn't still love him; she shouldn't give him a second chance. She should hate him and push him out the door right now, but she couldn't.

"I-I didn't mean to be gone so long," the Doctor said gently as he placed a hand on Clara's cheek and stroked it softly with his thumb. Clara sighed and couldn't help but lean into his touch as he continued, "I'm not going to blame the TARDIS like I probably should…I-I shouldn't have dropped you off in the first place…I hope you still love me because I still love you…"

Clara's heart instantly melted as she looked up into his eyes and murmured, "Oh, Doctor…I never stopped…" She grasped the back of his neck and pulled him down, pressing her lips against his as she kissed him. She smiled into the kiss when he started to squirm a little and flap his arms, but after a little while, he finally began to still as he wrapped his arms tightly around her middle.

They leisurely separated after a few more moments as the Doctor pressed his lips against her forehead and left them there. Clara kept her eyes closed as she sighed and leaned forward. She took his hands and laced her fingers with his.

Clara moved away, if only a little, so she could look into his eyes as a smirk worked its way across her face. It had only been four months for the Doctor, and he still recognized that look into her eyes. She let go of one of his hands and turned around as she led him into her bedroom.

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When Clara woke up, she felt the strange but not entirely unfamiliar and foreign feeling of an arm draped over her bare waist, and a chest pressed against her back, skin to skin. At first, she was too drowsy to completely process the previous night's events as she felt the other person stir, and she mumbled questioningly, "Simon?"

"_Simon?_" A familiar voice asked in response, and it wasn't Simon. Simon was American, and this voice had a refreshing British accent. "Who is _Simon_?"

The Doctor moved up so he was supporting himself on his elbow as he leaned over her and looked down at her. Clara glanced up at him before leaning away and turned her face into the pillow to hide it from his view as she replied, "No one…" She knew he wouldn't believe her.

"Clara, you wouldn't have said it if it was no one," the Doctor replied simply as he reached down and gently turned her head so she was looking at him. She tried to hold her head back but she finally gave in as she turned her eyes to look into his.

"Why won't you tell me?"

"Because I don't want to hurt you…"

Clara knew he was smart enough to figure it out, and his wit didn't disappoint her expectations as the Doctor rolled onto his back. Clara turned over so she could look at him to find him staring at the ceiling. His eyes were distant, making it obvious that he was deep in thought. Clara found herself in a switched position with her trying to get information as she asked, "Doctor?"

"You and him, eh?" The Doctor asked as he looked at her. Clara could see the pain in his eyes, but what was he expecting? He had been gone for five years, and even though she missed him terribly every day and still loved him very much, he couldn't possibly think that she had waited. After the first few months without him returning, she didn't think he was ever coming back, and Beckett kept telling her that she needed to move on.

"For a time…yes," Clara replied as the Doctor nodded slowly before asking, "Did you…Did you a-and him…Was he _here_?" He wasn't blushing, but Clara could tell that he was flustered and wary. His worries were confirmed when Clara nodded.

"Doctor, you were gone for _five_ years…" Clara added softly as she moved closer to him and looked down at him. "I moved on with my life and got a new job. I made new friends. Beckett kept telling me I had to move on with my love life too."

"I can understand that," the Doctor replied, before his brow furrowed together and he looked at her questioningly, "Beckett?"

Clara smiled, and the Doctor could tell that she must have gotten close to this Beckett, whoever he or she was. She ran her fingers through his hair absentmindedly as her smile widened, and she replied, "She took me in when I first got here. You dropped me off right in front of her fiancé's vacation house in the Hamptons."

"Sorry 'bout that," the Doctor added, and Clara couldn't help but smile as she kissed him softly and replied, "I know…"

She then grinned and commented flirtatiously, "Thank God it's Saturday."

The Doctor caught on almost instantly, but he fought off his usual flustered "fourteen year old" instincts, albeit a deep blush still colored his face from his ears to his cheeks. He gave her a look and smiled as he asked, "What do you want to do, Miss Clara? Any plans?"

"Plans? Who needs plans? You certainly never use them," Clara replied teasingly as she moved over him and brushed her hair over her shoulders. The Doctor pretended to be insulted as his eyebrows knitted together, and he responded indignantly, "I beg to differ. I have used plans before."

"Really?" Clara asked as she sat up a little straighter and drummed her fingernails on his chest. "Give me an example that I would remember."

"…Shut up!"

"Exactly!"

Clara then leaned down and kissed him as a realization hit her. There was something different about her Doctor. He wasn't acting like the nervous and embarrassed fourteen year old who had never kissed a girl before that he usually did. He wasn't flustered, but rather…_confident_, more open, in a way. He had changed, but, then again, so had she.

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**AUTHOR'S NOTE:**** So! Did you like it? I hope you did. I am in love with this story. I really like it, but it does matter to me if you liked it, so please review! :D Also, it wasn't that long of a chapter so I apologize for that. Chapter 2 should be up soon. I just have to finish writing it, then I have to type it up and upload it. Might take me a few days, so definitely don't get your hopes up that it will be up tomorrow because it definitely won't be up tomorrow. Maybe Thursday, Friday, or Saturday, but no promises. Anyways! You know the drill! Review = preview!**


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